Following the tragedy in Badenweiler, Sydney remains shattered after watching four CIA agents die in a plant explosion – triggered by Dixon as part of their SD-6 mission. She continues to struggle with a truth about SD-6 she cannot share with her fellow agent, while Vaughn convinces her that Dixon's life and family would be at peril if she ever crossed that line.
Upon returning, Sydney learns that Jack will now be working alongside her at SD-6. But after looking into her father's CIA file – given to her by Vaughn – she visits the widow of FBI Agent Calder, and begins to form an opinion that Jack's suspicious activities led to the death of her mother 20 years earlier – and this creates an even deeper tension between them.
The CIA continues to download SD-6's database though a worm previously implanted into their network via an invisible software control – unfortunately, Marshall reports the leak to Sloane who immediately suspects a mole from within.
Meanwhile, Charlie finally tells Francie his secret. He is not cheating on her, but has been pursuing his dream to become a professional singer. Francie has never even heard Charlie hum – she fears his humiliation, if it turns out he's on the wrong path. But he invites her to his debut at a local club, and her fears are assuaged when she hears his beautiful voice.
Will also uncovers the true identity of the woman who formerly claimed to be Kate Jones and to have had an affair with Danny. But when he surprises her at her door, she pepper-sprays him, terrified, sending him away. Later, she calls to explain she was paid to impersonate Kate – but when Will tries to meet her again for more details, he finds her apartment now emptied...
Sydney and Dixon's current mission is to recover one of FTL's genetically secured encoder devices – a highly sophisticated piece of cryptology equipment – from an operative named Smythe, who also owns a photo gallery in London. Dixon impersonates a wealthy buyer, distracting Smythe long enough for Sydney to break into the owner's highly secure offices, while eluding a menacing guard, and to recover the device. With the encoder in SD-6's possession, Marshall discovers it works by single-user DNA, sampled via a speck of skin from the recipient's fingertip.
SD-6 needs the fingertip of Gareth Parkashoff, now deceased, and whose burial location is unknown except to his assassin. In the guise of a patient, Sydney must infiltrate the asylum in Bucharest where his killer, Martin Shepard has been recently committed. With the aid of SD-6 Agent Fisher, posing as the physician committing her, Sydney's mission is to trigger Shepard for the body's coordinates by reciting a poem by John Donne, a known key from this assassin's programming.
Sydney is admitted upon their arrival in Romania...but her discharge will prove to much more complex, for only too late does the CIA discover that this institute is also run by Kreshnik, a K-Directorate agent. And when Sydney finds Agent Fisher with his throat slashed, the gates to this institution appear to be sealed for good...